Ontologies

The Phenoscape project is coordinating the development and integration of multispecies and single species anatomy ontologies for vertebrates, with taxonomic focus on teleosts, zebrafish, amphibians, Xenopus, amniotes, and mouse. These ontologies are publicly available and being used and extended by the community (view the list). Where possible, we are also reusing external ontologies (e.g., PATO) from the broader biological community for the greatest interoperability across data types. The development of these ontologies follows OBO Foundry principles as much as possible, including reuse of ontology terms (by import or MIREOT) as the preferred mechanism for using shared terms. These anatomy ontologies are available from the OBO CVS-based version-control system, from which they are regularly loaded into the NCBO BioPortal where they can be readily browsed, searched, and visualized. The ontologies are also available for download as .obo files from OBO Foundry and can also be viewed using the OBO-Edit desktop software.

The VAO will be imported into TAO, AAO, and AMAO. However, the existing model organism databases are largely hardcoded to reference identifiers for their own ontologies (e.g., MGI database reads MA term identifiers). In the long term, we will be exploring how to import terms into these ontologies. In the interim, the existing MOD vertebrate ontologies will continue to create equivalent terms from other ontologies and keep links to them using a cross-referencing strategy to external ontology identifiers.

We hold regular project anatomy ontology conference calls to discuss development with the curators of these ontologies. The limb/fin branch is the focus of ontology development in year 1 across the various ontologies described below.

Anatomy Ontologies

Vertebrate Musculoskeletal Anatomy Ontology (VAO)

VAO contains terms representing structures in the musculoskeletal system of vertebrates. It references terms from the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO) Biological Process, Cell Ontology (CL), and the Phenotype and Trait Ontology (PATO). VAO can be downloaded at the OBO Foundry and browsed at BioPortal.

Ontology update requests can be made on the Vertebrate Anatomy term request tracker. Requests are forwarded to the vertebrate anatomy mailing list.

• Submit term requests to the vertebrate anatomy request tracker

• Subscribe to the vertebrate anatomy mailing list for notification of term requests

Development

VAO will be expanded to include terms in the muscular and skeletal systems that are shared by two or more multispecies vertebrate ontologies. These shared terms will be imported into the multispecies ontologies. For example, ‘femur’, a term applicable to AAO and AMAO, will be added to VAO and imported into AMAO (Year 1) and AAO (Year 2). Shared terms that already exist in multispecies ontologies will be obsoleted, given a "replaced_by" relationship to the relevant VAO term, and the shared term subsequently imported into the ontology. Terms shared by a multispecies ontology and its corresponding single-species ontology (e.g., AAO and XAO) would also ideally be imported from the multispecies ontology into the single species ontology (or rather, a single ontology for that taxonomic group could be used). However, because MODs currently cannot import terms, shared terms will instead be duplicated in single species ontologies and cross-referenced to the term in the external ontology. For example, because XAO and AAO both contain ‘radio-ulna’, the term XAO term will cross-reference the AAO ID for radio-ulna.

New skeletal terms for the limb/fin and cranial skeleton have and will continue to be added based on work done at the Phenotype RCN Vertebrate Working Group meeting in Boulder, CO (June 1-3, 2011) and from ongoing work here: [1]

Amniote Anatomy Ontology (AMAO)

AMAO is a new anatomy ontology being developed for amniotes. It will import skeletal terms from VAO and non-skeletal terms from the Uber Anatomy Ontology (Uberon).

It wil be available at: and the Tracker will be at:

Development

Under construction.

Amphibian Anatomy Ontology (AAO)

AAO is a multispecies ontology for amphibian anatomy. It will be used to annotate characters from the amphibian systematics literature. Download AAO from the OBO Foundry and browse at BioPortal

See the AAO development plan for more details on its release schedule and development.

Mouse Adult Gross Anatomy (MA)

The Adult Mouse Anatomy (MA) ontology contains terms that represent structures in the postnatal mouse (Mus) and is used to annotate gene expression and phenotypes for the mouse at Mouse Genome Informatics (MGI) and other resources. The MA is available for download at the OBO Foundry and can be browsed using the Mouse Anatomy Browser. Term requests can be submitted on the mouse anatomy tracker

See the MA development plan for more details on its release schedule and development.

Teleost Anatomy Ontology (TAO)

TAO is a multi-species ontology for teleost fishes that was initialized with terms from the Zebrafish Anatomical Ontology (ZFA). The development of the TAO currently focuses on the skeletal system because it varies significantly across fishes, is well-preserved in fossil specimens, and it is often the focus of morphologically-based evolutionary studies in ichthyology. The development of the TAO is described in Dahdul et al. (2010). Download TAO from the OBO Foundry and browse at BioPortal. Term requests can be submitted to the TAO tracker.

See the TAO development plan for more details on its release schedule and development.

Xenopus Anatomy Ontology (XAO)

XAO contains terms that represent anatomical structures for the model organism Xenopus laevis (African clawed frog). Xenbase uses XAO to annotate Xenopus gene expression and phenotypes. XAO can be downloaded at the OBO Foundry and browsed at the BioPortal.

See the XAO development plan for more details on its release schedule and development.

Zebrafish Anatomical Ontology (ZFA)

ZFA is used by ZFIN to annotate mutant phenotypes for the model organsim zebrafish (Danio rerio). ZFA can be downloaded from the OBO Foundry and browsed at the BioPortal. Term requests can be submitted to the ZFA tracker.

See the ZFA development plan for more details on its release schedule and development.

Taxonomy Ontologies

Teleost Taxonomy Ontology (TTO)

Phenotypes are associated with species using a taxonomy ontology, the Teleost Taxonomy Ontology (TTO) derived from the Catalog of Fishes (see also the representation on BioPortal, which can be navigated on-line). The TTO is updated in concert with Catalog of Fishes updates. Changes to the TTO relative to the latest version generated from a dump from the Catalog of Fishes are documented TTO_Changes.

Amphibian Taxonomy Ontology (ATO)

The ATO is derived from the AmphibiaWeb list, which provides both taxonomy and some synonyms from ITIS and the IUCN redlist.

Vertebrate Taxonomy Ontology (VTO)

The Vertebrate Taxonomy Ontology includes the TTO, ATO, as well as a new Amniote Taxonomy Ontology. An initial release, including TTO and ATO, but using pan-vertebrate resources (see below) rather than a separate AmTO was made in May 2011. This taxonomy covers vertebrates and was built by starting with the NCBI taxonomy for vertebrates and splicing in TTO (except hagfish), ATO, and the IOC taxonomy of living birds. Synonyms from ITIS and Catalog of Life were attached if the primary name matched a name in the existing taxonomy. Subspecies names were added to their parent species as synonyms (not subclasses). The taxonomy is currently in the OBO format used for TTO and ATO, which includes the use of the Taxonomic Rank Vocabulary to tag taxa with specified rank.

Other Taxonomic Resources

Amniotes

• Birds The IOC checklist provides a current taxonomy and common names, but no taxonomic synonyms.
• Mammals Wilson and Reader (1993) is the standard, but the available electronic version of their taxonomy is IP encumbered.

Fossil Taxa

• Paleobiology Database This covers all groups represented in the fossil record - we have implemented a way to incorporate bulk taxonomy downloads in the VTO. We are still somewhat uncertain about how hierarchies are (dynamically) built in this resource.

Taxonomic (hierarchy) Resources

• NCBI This was used to fill in the gaps (non-avian amniotes) in the current proposed VTO. This provides taxonomy for GenBank submissions (including fossil taxa), but does not claim to be an authoritative source (and generally doesn't cover taxa that have not been submitted). It does provide some taxonomic synonyms as well.
• ITIS Has some vetting by area experts, but coverage is not complete (nor uncontroversial).
• Catalogue of Life Claimed to incorporate all of ITIS plus Species2000. Updated quarterly.

Nomenclature Resources

These can provide links to additional synonyms and resources (e.g., TTO uses fishbase to provide common names and links to their pages). Taxonomic synonyms are particularly useful as aids to data curation, but common names can assist users in browsing the website. Taxonomic resources (above) can be used as sources of names as well.

• Fishbase - their taxonomy is close to TTO (both based on Catalog of Fishes), but TTO uses it strictly as a name resource.
• Global Names Index (GNI) - Extensive list of names but no hierarchy.

Additional documentation

• Documenting taxon concepts used in a publication
• Taxonomy ontology: ranks, unknown/unnamed species, & related issues
• Ambiguous specimen information: annotating phenotypes for specimens or species (also called the Hypodigm problem)

Taxonomic Rank Vocabulary

During 2010, we released a separate Taxonomic Rank Vocabulary (TAXRANK), and removed all rank terms (e.g., family, genus, etc.) from the taxa within the TTO. Taxa in the TTO specify their ranks as property values via the metadata relation has_rank, but the object of the has_rank links is contained in the TAXRANK vocabulary.

Developing TAXRANK as a vocabulary, rather than an ontology (e.g., by defining an ordering relation between ranks) should facilitate its reuse in other taxonomic ontologies. Developing a cross-authority (e.g., ICZN, ICBN, etc.) ontology of ranks may be possible, but there does not appear to be a compelling need for such an ontology. The TAXRANK vocabulary can be browsed at Bioportal.

• Browse TTO at BioPortal
• Download TTO from Bioportal or OBO Foundry (use OBO Edit desktop software to open and view .obo file).

Fish Collection Codes Ontology

There is a vocabulary of fish collections, based on a list used in Catalog of Fishes, though with a few additions listed on the Fish Collection Updates page. The master list, from which the OBO ontology is generated is available as a google docs spreadsheet. It has been augmented with links to entries in the Biodiversity Collections Index.

The current release, as used in Phenex is Fish Collection Abbreviations

Shared Ontologies

These ontologies listed below were initiated by the model organism communities. Phenoscape is actively involved in extending these ontologies.

Phenotype and Trait Ontology

• Phenotype and Trait Ontology (PATO)

Evidence Code Ontology

• Evidence Code Ontology

Relations Ontology

• OBO-relations

Spatial Ontology

• Spatial Ontology

Comparative Data Analysis Ontology

CDAO is developed by the EvoInfo working group at NESCent, and is being used within the Phenoscape OBD data repository.

• CDAO